esmfold2: return each CCD ligand component as its own residue

[daylight-00]

A ligand given as several CCD codes comes back from fold() as one residue named after its first component:

LigandInput(id="B", ccd=["NAG", "BMA"])
# complex.sequence: [..., "NAG"]          # both components' atoms under one name
# with this PR:     [..., "NAG", "BMA"]

The tokenizer already keeps each component's residue_index; only the output builder threw it away.

• Non-polymer tokens are now grouped by residue_index, the same way atom-tokenized polymer residues (MSE, HYP, ...) already are. The two branches share one loop and differ only in the hetero flag.
• SMILES ligands, single-CCD ligands and polymers come back exactly as before. The docstring described the old collapse, so this is a deliberate behavior change for multi-component ligands only.
• Bonus fix: to_mmcif() keys entities on residue names, so ["NAG", "NAG"] and ["NAG", "BMA"] were written as the same entity. They no longer are.

Tested with a new tests/models/esmfold2_output_test.py (needs the CCD pickle): the two multi-component cases fail on main and pass here, and the single-component case passes on both. No new failures in prepare_input_test.py, esmfold2_inputs_test.py or esmfold2_cpu_only_test.py; ruff and ty are clean.

[Copilot]

Copilot review overview

🔵 Needs a closer look

The experimental output path and empty-CCD fallback still need correction.

Review effort: Lite
Findings: None

What changed in this PR

This PR updates ESMFold2 output construction so multi-component CCD ligands are returned as separate residues and distinct mmCIF entities.

Changes:

• Groups ligand components by residue_index.
• Preserves hetero flags and existing behavior for other ligand types.
• Adds regression tests for residue grouping and entity separation.

File	Summary
tests/​models/​esmfold2_output_test.py	Adds coverage for multi-component ligand residues and entity mapping.
esm/​models/​esmfold2/​output.py	Groups ligand components into separate residues and updates entity handling.

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